Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 289 Consequences of the Domestication of Man’s Best Friend, The Dog SUSANNE BJÖRNERFELDT ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 UPPSALA ISBN 978-91-554-6854-5 2007 urn:nbn:se:uu:diva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ll knowledge, the totality of all questions and answers, is contained in the dog. FRANZ KAFKA, Investigations of the dog Cover photos by S Björnerfeldt List of Papers This thesis is based on the following papers, referred to by their Roman numerals throughout the text. I Björnerfeldt S*, Webster MT*, Vilà C (2006) Relaxation of selective constraint on dog mitochondrial DNA following domestication. Genome Research 16:990–994. * Equal contribution. II Sundqvist A-K, Björnerfeldt S, Leonard JA, Hailer F, Hedhammar Å, Ellegren H, Vilà C (2006) Unequal contribution of sexes in the origin of dog breeds. Genetics 172:1121–1128. III Björnerfeldt S, Hailer F, Nord M, Vilà C Disruptive selection within dog breeds. (Submitted) IV Björnerfeldt S, Hailer F, Vilà C Estimation of recent gene flow in metapopulations: using poodles as a model organism. (Manuscript) V Björnerfeldt S, Vilà C (in press). Evaluation of methods for single hair DNA amplification. Conservation Genetics, published online: 28 October 2006. Copyright notices: Paper I, II and V are reproduced with kind permission of: © Cold Spring Harbor Laboratory Press 2006 (Paper I) © the Genetics Society of America 2006 (Paper II) © Springer Science and Business Media 2006 (Paper V) Additional papers not included in the thesis: Vilà C, Sundqvist A-K, Flagstad O, Seddon J, Björnerfeldt S, Kojola I, Casulli A, Sand H, Wabakken P, Ellegren H (2003) Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. Proceedings of the Royal Society of London. B: biological sciences 270:91–97. Lindberg J*, Björnerfeldt S*, Saetre P, Svartberg K, Seehuus B, Bakken M, Vilà C, Jazin E (2005) Selection for tameness has changed brain gene expression in silver foxes. Current Biology 15:R915–R916. * Equal contribution. Seddon JM, Sundqvist A-K, Björnerfeldt S, Ellegren H (2006) Genetic identification of immigrants to the Scandinavian wolf population. Conservation Genetics 7:225–230. Contents Introduction...................................................................................................11 Man’s best friend......................................................................................11 Dog domestication....................................................................................12 Definition of domestication and domestic animals..............................12 Origin of domestic dogs.......................................................................13 The first domestication events – when, where and how many? ..........14 Changes associated with domestication...............................................17 The dog (Canis familiaris) today .............................................................21 Species.................................................................................................21 The Family Canidae.............................................................................21 The ancestor of the domestic dog: The Grey Wolf..............................22 The Dog Genome.................................................................................23 The diversity of dogs ...........................................................................24 Dogs as a model organism for the study of human diseases................26 Dogs as a model organism for the study of biodiversity .....................27 Genetic markers used in domestication studies ............................................29 Mitochondrial DNA .................................................................................29 Y chromosome .........................................................................................30 Autosomal microsatellites ........................................................................31 Research aims ...............................................................................................32 Present Investigations ...................................................................................33 Paper I. Relaxation of selective constraint on dog mitochondrial DNA following domestication...........................................................................33 Material and methods ..........................................................................33 Results and discussion .........................................................................34 Paper II. Unequal contribution of sexes in the origin of dog breeds........36 Material and methods ..........................................................................36 Results and discussion .........................................................................37 Paper III. Disruptive selection within dog breeds ....................................38 Material and methods ..........................................................................39 Results and discussion .........................................................................40 Paper IV. Estimation of recent gene flow in metapopulations: using poodles as a model organism....................................................................41 Material and methods ..........................................................................41 Results and discussion .........................................................................43 Paper V. Evaluation of methods for single hair DNA amplification........43 Material and methods ..........................................................................44 Results and discussion .........................................................................44 Concluding remarks......................................................................................46 Future prospects............................................................................................47 Svensk sammanfattning ................................................................................48 Bakgrund ..................................................................................................48 Hundens utveckling från domesticering till rasbildning ..........................48 Artikel I. Ett försvagat selektivt tryck på mitokondriens DNA som ett led av domesticeringen...................................................................................50 Artikel II. Ojämn könsfördelning vid bildandet av hundraser .................50 Artikel III. Riktad selektion leder till struktur inom hundraser................51 Artikel IV. Uppskattnig av genflöde inom en metapopulation, genom att använda pudel som modell.......................................................................52 Artikel V. Utvärdering av metoder för att amplifiera DNA från enstaka hårstrån.....................................................................................................53 Slutsats .....................................................................................................53 Acknowledgements.......................................................................................54 References.....................................................................................................56 Abbreviations AKC American Kennel Club AMOVA Analysis of Molecular Variance bp Base pair(s) d-loop Displacement loop (mitochondrial control region) dN Nonsynonymous substitution rate DNA Deoxyribonucleic acid dS Synonymous substitution rate FCI Fédération Cynologique Internationale; World Canine Organisation Gb Gigabase (109 base pairs) kb Kilobase (103 base pairs) LD Linkage disequilibrium Mb Megabase (106 base pairs) MHC Major histocompatibility complex ML Maximum-likelihood mtDNA Mitochondrial DNA NCBI National Center for Biotechnology Information NJ Neighbour-joining PCR Polymerase chain reaction RNA Ribonucleic acid rRNA Ribosomal RNA SNP Single nucleotide polymorphism tRNA Transfer RNA WGA Whole Genome Amplification Introduction He is your friend, your partner, your defender, your dog. You are his life, his love, his leader. He will be yours, faithful and true, to the last beat of his heart. You owe it to him to be worthy of such devotion. UNKNOWN Man’s best friend We are today surrounded by more than 400 million dogs worldwide; purebred, mongrel and feral dogs (Coppinger and Coppinger 2001), all of